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Yorodumi- PDB-2nnc: Structure of the sulfur carrier protein SoxY from Chlorobium limi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nnc | ||||||
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Title | Structure of the sulfur carrier protein SoxY from Chlorobium limicola f thiosulfatophilum | ||||||
Components | Sulfur covalently-binding protein | ||||||
Keywords | LIGAND BINDING PROTEIN / sulfur binding protein / SoxY / beta sandwich / green sulfur bacterium | ||||||
Function / homology | Function and homology information SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Chlorobium limicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / MIRAS / Resolution: 2.14 Å | ||||||
Authors | Stout, J. / Van Driessche, G. / Savvides, S.N. / Van Beeumen, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure. Authors: Stout, J. / Van Driessche, G. / Savvides, S.N. / Van Beeumen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nnc.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nnc.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 2nnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nnc_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2nnc_full_validation.pdf.gz | 462 KB | Display | |
Data in XML | 2nnc_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2nnc_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nnc ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nnc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13055.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium limicola (bacteria) / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8RLX2 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Ammonium phosphate, sodium acetate, DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.14→99 Å / Num. obs: 13122 / % possible obs: 98.1 % / Observed criterion σ(I): 5.6 / Redundancy: 7.81 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.4 | |||||||||||||||
Reflection shell | Resolution: 2.14→2.2 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.6 / Num. unique all: 831 / % possible all: 97.8 |
-Phasing
Phasing | Method: MIRAS | |||||||||||||||||||||||||||
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Phasing MIR | Resolution: 3→25 Å / FOM: 0.49 / Reflection: 4946 | |||||||||||||||||||||||||||
Phasing MIR shell |
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-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.14→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.828 / SU ML: 0.189 / SU R Cruickshank DPI: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.075 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.141→2.196 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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